WASHINGTON — A federal agency in charge of investigating whistleblower complaints is scrutinizing the military’s top crime lab, already troubled by sloppy evidence handling and botched analysis of DNA.

The Office of Special Counsel agreed last month to look into claims that the lab had retaliated against its former firearms-branch chief, in part for cooperating with investigators who were looking into allegations of misconduct by lab officials.

The branch chief, Donald Mikko, resigned last week after 21 years at the lab and 10 years as a manager. His lawyer, Peter Lown, said his client felt forced to leave.

“He’s undergone what is approaching two years of escalating harassment and retaliation,” Lown said. “The environment at the lab has become so hostile that in the interest of his well-being he had to leave.”

The upheaval comes as the lab’s director, Larry Chelko, also announced last week that he’s retiring after more than 18 years, the Army Criminal Investigation Command confirmed. The U.S. Army Criminal Investigation Laboratory is the military’s most important forensics facility, handling more than 3,000 criminal cases a year.

“Mr. Chelko is retiring after a distinguished 36 years of dedicated and valuable service to this nation, the Army and USACIL,” command officials said in an emailed statement. “We strongly reject any suggestion that his retirement is connected to anything beyond normal career progression and a well-deserved retirement.”

During Chelko’s recent tenure, the lab has been the target of numerous investigations, including an ongoing Pentagon inspector general inquiry that was launched last year in response to McClatchy’s series of stories on problems with evidence-handling at the lab. Through it all, the command continued to support his leadership. Before the scrutiny, the secretary of the Army gave Chelko a 2010 Exceptional Civilian Service Award, which recognizes a pattern of excellence and achievement.

McClatchy has written more than a dozen stories about the lab since March 2011 detailing the misconduct of two former analysts, who made serious errors during DNA and firearms testing and who later were found to have falsified and destroyed documents when confronted with the problems.

Meanwhile, a growing number of employees have filed complaints against Chelko and other leaders at the lab. In less than four years, at least seven internal investigations have been launched and eight complaints filed against managers. Employees say the turmoil has distracted them from their mission of analyzing evidence. An employee satisfaction survey was conducted in the wake of the complaints. The command refused to release a copy to McClatchy immediately, saying a reporter would have to file an open records request for it.

In one of the latest internal inquiries, Mikko was interrogated for about four hours and questioned about his contacts with McClatchy, according to Lown. The command launched the inquiry after McClatchy published a story late last year about the lab losing evidence. In March, his supervisor recommended Mikko’s firing as a result of the inquiry, even though investigators didn’t determine who’d spoken to McClatchy about the problems.

The Criminal Investigation Command says it’s never targeted anyone for talking to the news media, and it asserts that McClatchy’s stories have overblown isolated mistakes and misconduct that shouldn’t reflect on the lab’s overall reputation.

But in his complaint to the Office of Special Counsel, Mikko alleged that lab officials punished him for cooperating with a complaint of racial discrimination filed by a black employee. Mikko also accused lab officials of retaliating against him for cooperating with an internal investigation into whether his supervisor had a conflict of interest. The supervisor was cleared of wrongdoing.

Recently, the lab agreed to settle allegations by its former attorney Lisa Kreeger that she was retaliated against for cooperating with the same racial discrimination complaint. Her attorney Charles Evans said he couldn’t disclose the terms of the settlement. Mikko’s retaliation compliant, meanwhile, is proceeding before a judge who oversees employment discrimination disputes.

The Criminal Investigation Command, abbreviated as CID, declined to comment on the allegations by its former branch manager and attorney, saying privacy laws prevented it from discussing the complaints.

“In short, individuals may bring their side of the story to the media, but CID cannot respond,” command officials said in a statement.

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